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. 2018 Jan;27(1):259-268.
doi: 10.1002/pro.3313. Epub 2017 Oct 27.

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Rocco Moretti  1 , Sergey Lyskov  2 , Rhiju Das  3   4 , Jens Meiler  1 , Jeffrey J Gray  2   5
Affiliations

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Rocco Moretti et al. Protein Sci. 2018 Jan.

Abstract

The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pKa determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org.

Keywords: design; molecular modeling; prediction; web server.

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Figures

Figure 1
Figure 1
ROSIE input elements. A: Example of a submission form. B: Example of the FileInput widget, customized for structure file loading. C: Example of the FileInput widget, after file selection. Icons of the submitted structures are shown. D: Example of the CheckboxInput and FloatInput widgets.
Figure 2
Figure 2
A ROSIE result page, showing output elements. A: The JobHeader widget provides details about the protocol run. B: The TopModels widget shows the selected result structures. Each structure can be downloaded by clicking on it. C: The ScorePlot widget displays a plot of two selected scores. Additional information for each point can be obtained by hovering over it. D: The ScoreTable widget. The results can be sorted by each column, and any particular structure can be downloaded by clicking its name.
See this image and copyright information in PMC

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References

    1. Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D (2017) Protein structure determination using metagenome sequence data. Science 355:294–298. - PMC - PubMed
    1. Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou F‐C, Ferre‐D'Amare AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin‐Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska‐Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Jr , Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams BII, Xiao Y, Xu X, Zhang D, Zok T, Westhof E (2017) RNA‐Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 23:655–672. - PMC - PubMed
    1. Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf‐Bryfogle J, Biswas N, Dunbrack RL, Jr , Gray JJ (2017) Modeling and docking of antibody structures with Rosetta. Nat Protoc 12:401–416. - PMC - PubMed
    1. Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ (2017) Modeling oblong proteins and water‐mediated interfaces with RosettaDock in CAPRI rounds 28–35. Proteins 85:479–486. - PMC - PubMed
    1. Alam N, Schueler‐Furman O (2017) Modeling peptide‐protein structure and binding using Monte Carlo sampling approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol 1561:139–169. - PubMed

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